Structure determination and characterization of the vitamin B6 degradative enzyme (E)-2-(acetamidomethylene)succinate hydrolase.

The gene identification and kinetic characterization of (E)-2-(acetamidomethylene)succinate (E-2AMS) hydrolase has recently been described. This enzyme catalyzes the final reaction in the degradation of vitamin B(6) and produces succinic semialdehyde, acetate, ammonia, and carbon dioxide from E-2AMS. The structure of E-2AMS hydrolase was determined to 2.3 A using SAD phasing. E-2AMS hydrolase is a member of the alpha/beta hydrolase superfamily and utilizes a serine/histidine/aspartic acid catalytic triad. Mutation of either the nucleophilic serine or the aspartate resulted in inactive enzyme. Mutation of an additional serine residue in the active site causes the enzyme to be unstable and is likely structurally important. The structure also provides insight into the mechanism of hydrolysis of E-2AMS and identifies several potential catalytically important residues.

[1]  Tingyi Wen,et al.  Crystal Structure of a Novel Esterase Rv0045c from Mycobacterium tuberculosis , 2011, PloS one.

[2]  T. Begley,et al.  Structure of the PLP degradative enzyme 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti MAFF303099 and its mechanistic implications. , 2009, Biochemistry.

[3]  L. Essen,et al.  The crystal structure of enamidase: a bifunctional enzyme of the nicotinate catabolism. , 2008, Journal of molecular biology.

[4]  K. Ohnishi,et al.  Gene identification and characterization of the pyridoxine degradative enzyme alpha-(N-acetylaminomethylene)succinic acid amidohydrolase from Mesorhizobium loti MAFF303099. , 2008, Journal of nutritional science and vitaminology.

[5]  T. Begley,et al.  PLP catabolism: identification of the 2-(Acetamidomethylene)succinate hydrolase gene in Mesorhizobium loti MAFF303099. , 2008, Biochemistry.

[6]  Gene identification and characterization of the pyridoxine degradative enzyme 4-pyridoxic acid dehydrogenase from the nitrogen-fixing symbiotic bacterium Mesorhizobium loti MAFF303099. , 2008, Journal of biochemistry.

[7]  Jeong-Sun Kim,et al.  High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement. , 2008, Journal of molecular biology.

[8]  H. Hayashi,et al.  Crystal Structure of Pyridoxamine-Pyruvate Aminotransferase from Mesorhizobium loti MAFF303099* , 2008, Journal of Biological Chemistry.

[9]  M. Hassler,et al.  Catalytic promiscuity in the alpha/beta-hydrolase superfamily: hydroxamic acid formation, C--C bond formation, ester and thioester hydrolysis in the C--C hydrolase family. , 2008, Chembiochem : a European journal of chemical biology.

[10]  C. Kinsland,et al.  PLP catabolism: identification of the 4-pyridoxic acid dehydrogenase gene in Mesorhizobium loti MAFF303099. , 2007, Bioorganic chemistry.

[11]  T. Begley,et al.  Gene identification and structural characterization of the pyridoxal 5'-phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from mesorhizobium loti MAFF303099. , 2007, Biochemistry.

[12]  T. Bugg,et al.  Investigation of a general base mechanism for ester hydrolysis in C-C hydrolase enzymes of the alpha/beta-hydrolase superfamily: a novel mechanism for the serine catalytic triad. , 2007, Organic & biomolecular chemistry.

[13]  K. Ohnishi,et al.  Molecular cloning, identification and characterization of 2-methyl-3-hydroxypyridine-5-carboxylic-acid-dioxygenase-coding gene from the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. , 2006, Journal of bioscience and bioengineering.

[14]  S. Wood,et al.  Catalytic role for arginine 188 in the C-C hydrolase catalytic mechanism for Escherichia coli MhpC and Burkholderia xenovorans LB400 BphD. , 2006, Biochemistry.

[15]  K. Ohnishi,et al.  Identification of a new tetrameric pyridoxal 4-dehydrogenase as the second enzyme in the degradation pathway for pyridoxine in a nitrogen-fixing symbiotic bacterium, Mesorhizobium loti. , 2006, Archives of biochemistry and biophysics.

[16]  F. Elmi,et al.  Stereoselective Esterase from Pseudomonas putida IFO12996 Reveals α/β Hydrolase Folds for d-β-Acetylthioisobutyric Acid Synthesis , 2005 .

[17]  K. Ohnishi,et al.  4-Pyridoxolactonase from a symbiotic nitrogen-fixing bacterium Mesorhizobium loti: cloning, expression, and characterization. , 2005, Biochimica et biophysica acta.

[18]  J. Cooper,et al.  The structure of the C-C bond hydrolase MhpC provides insights into its catalytic mechanism. , 2005, Journal of molecular biology.

[19]  S. Wood,et al.  Catalytic mechanism of C-C hydrolase MhpC from Escherichia coli: kinetic analysis of His263 and Ser110 site-directed mutants. , 2005, Journal of molecular biology.

[20]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[21]  A. Tocilj,et al.  Biological Crystallography Structure of an Aryl Esterase from Pseudomonas Fluorescens , 2022 .

[22]  K. Ohnishi,et al.  The nitrogen-fixing symbiotic bacterium Mesorhizobium loti has and expresses the gene encoding pyridoxine 4-oxidase involved in the degradation of vitamin B6. , 2004, FEMS microbiology letters.

[23]  Jack F Kirsch,et al.  Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. , 2003, Annual review of biochemistry.

[24]  Hiroshi Habe,et al.  Crystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme). , 2003, Biochemical and biophysical research communications.

[25]  Thomas C. Terwilliger,et al.  Electronic Reprint Biological Crystallography Automated Main-chain Model Building by Template Matching and Iterative Fragment Extension , 2022 .

[26]  George M. Sheldrick,et al.  Macromolecular phasing with SHELXE , 2002 .

[27]  L. Hedstrom.  Serine protease mechanism and specificity. , 2002, Chemical reviews.

[28]  George M Sheldrick,et al.  Substructure solution with SHELXD. , 2002, Acta crystallographica. Section D, Biological crystallography.

[29]  S H Kim,et al.  Crystal structure and mechanism of catalysis of a pyrazinamidase from Pyrococcus horikoshii. , 2001, Biochemistry.

[30]  Thomas C. Terwilliger,et al.  Electronic Reprint Biological Crystallography Maximum-likelihood Density Modification , 2022 .

[31]  Y. Nakamura,et al.  Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. , 2000, DNA research : an international journal for rapid publication of reports on genes and genomes.

[32]  M. Nardini,et al.  α/β Hydrolase fold enzymes : the family keeps growing , 1999 .

[33]  A. Goldman,et al.  Of barn owls and bankers: a lush variety of alpha/beta hydrolases. , 1999, Structure.

[34]  Patrice Gouet,et al.  ESPript: analysis of multiple sequence alignments in PostScript , 1999, Bioinform..

[35]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[36]  W. Lipscomb,et al.  Detection and use of pseudo-translation in determination of protein structures. , 1998, Acta crystallographica. Section D, Biological crystallography.

[37]  H. Hecht,et al.  Structural investigation of the cofactor-free chloroperoxidases. , 1998, Journal of molecular biology.

[38]  Chris Sander,et al.  Touring protein fold space with Dali/FSSP , 1998, Nucleic Acids Res..

[39]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[40]  F M Vellieux,et al.  Noncrystallographic symmetry averaging in phase refinement and extension. , 1997, Methods in enzymology.

[41]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[42]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[43]  W. C. Still,et al.  A rapid approximation to the solvent accessible surface areas of atoms , 1988 .

[44]  E. Snell,et al.  Enzymes of vitamin B6 degradation. Purification and properties of two N-acetylamidohydrolases. , 1985, The Journal of biological chemistry.

[45]  M. M. Bradford.  A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[46]  B. Matthews.  Solvent content of protein crystals. , 1968, Journal of molecular biology.

[47]  D. B. Hood,et al.  The metabolism of vitamin B6. , 1942 .